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Fix Memory Leak #393

Merged
merged 4 commits into from
Oct 22, 2024
Merged

Fix Memory Leak #393

merged 4 commits into from
Oct 22, 2024

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varunagrawal
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I ran leaks on the testForwardKinematics executable and I got the following memory leak reported.

>> leaks --atExit -- ./testForwardKinematicsFactor
testForwardKinematicsFactor(1381) MallocStackLogging: could not tag MSL-related memory as no_footprint, so those pages will be included in process footprint - (null)
testForwardKinematicsFactor(1381) MallocStackLogging: recording malloc and VM allocation stacks using lite mode
There were no test failures
Process:         testForwardKinematicsFactor [1381]
Path:            /Users/USER/*/testForwardKinematicsFactor
Load Address:    0x102778000
Identifier:      testForwardKinematicsFactor
Version:         0
Code Type:       ARM64
Platform:        macOS
Parent Process:  leaks [1380]

Date/Time:       2024-10-22 09:50:43.803 -0400
Launch Time:     2024-10-22 09:50:42.962 -0400
OS Version:      macOS 14.6.1 (23G93)
Report Version:  7
Analysis Tool:   /Applications/Xcode.app/Contents/Developer/usr/bin/leaks
Analysis Tool Version:  Xcode 16.0 (16A242d)

Physical footprint:         10.2M
Physical footprint (peak):  28.1M
Idle exit:                  untracked
----

leaks Report Version: 4.0, multi-line stacks
Process 1381: 263 nodes malloced for 44 KB
Process 1381: 13 leaks for 4928 total leaked bytes.

STACK OF 1 INSTANCE OF 'ROOT CYCLE: <std::__shared_ptr_emplace<gtdynamics::Link>>':
21  dyld                                  0x18976eef4 start + 1868
20  dyld                                  0x189770010 dyld4::prepare(dyld4::APIs&, dyld3::MachOAnalyzer const*) + 3156
19  dyld                                  0x1897a9e3c dyld4::APIs::runAllInitializersForMain() + 464
18  dyld                                  0x189786b78 dyld4::Loader::runInitializersBottomUpPlusUpwardLinks(dyld4::RuntimeState&) const + 420
17  dyld                                  0x18978a698 dyld4::Loader::runInitializersBottomUpPlusUpwardLinks(dyld4::RuntimeState&) const::$_1::operator()() const + 116
16  dyld                                  0x189786984 dyld4::Loader::runInitializersBottomUp(dyld4::RuntimeState&, dyld3::Array<dyld4::Loader const*>&) const + 220
15  dyld                                  0x18978cbc0 dyld4::JustInTimeLoader::runInitializers(dyld4::RuntimeState&) const + 36
14  dyld                                  0x18978653c dyld4::Loader::findAndRunAllInitializers(dyld4::RuntimeState&) const + 564
13  dyld                                  0x1897c8880 dyld3::MachOAnalyzer::forEachInitializer(Diagnostics&, dyld3::MachOAnalyzer::VMAddrConverter const&, void (unsigned int) block_pointer, void const*) const + 516
12  dyld                                  0x1897bb394 dyld3::MachOFile::forEachSection(void (dyld3::MachOFile::SectionInfo const&, bool, bool&) block_pointer) const + 192
11  dyld                                  0x18976b2fc dyld3::MachOFile::forEachLoadCommand(Diagnostics&, void (load_command const*, bool&) block_pointer) const + 300
10  dyld                                  0x1897bc400 invocation function for block in dyld3::MachOFile::forEachSection(void (dyld3::MachOFile::SectionInfo const&, bool, bool&) block_pointer) const + 496
9   dyld                                  0x1897c8d6c invocation function for block in dyld3::MachOAnalyzer::forEachInitializer(Diagnostics&, dyld3::MachOAnalyzer::VMAddrConverter const&, void (unsigned int) block_pointer, void const*) const + 340
8   dyld                                  0x18978a608 invocation function for block in dyld4::Loader::findAndRunAllInitializers(dyld4::RuntimeState&) const::$_0::operator()() const + 168
7   testForwardKinematicsFactor           0x102789198 _GLOBAL__sub_I_testForwardKinematicsFactor.cpp + 640
6   testForwardKinematicsFactor           0x102780a9c simple_rr::getRobot() + 156
5   libgtdynamics.dylib                   0x102e36ec8 gtdynamics::CreateRobotFromFile(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, bool) + 716
4   libgtdynamics.dylib                   0x102e3731c gtdynamics::ExtractRobotFromSdf(sdf::v12::Model const&) + 128
3   libgtdynamics.dylib                   0x102e3655c gtdynamics::LinkFromSdf(unsigned char, sdf::v12::Link const&) + 408
2   libgtdynamics.dylib                   0x102e415a4 std::__1::shared_ptr<gtdynamics::Link> std::__1::allocate_shared[abi:ne180100]<gtdynamics::Link, std::__1::allocator<gtdynamics::Link>, unsigned char&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, double, Eigen::Matrix<double, 3, 3, 0, 3, 3>&, gtsam::Pose3 const&, gtsam::Pose3 const&, void>(std::__1::allocator<gtdynamics::Link> const&, unsigned char&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&&, double&&, Eigen::Matrix<double, 3, 3, 0, 3, 3>&, gtsam::Pose3 const&, gtsam::Pose3 const&) + 64
1   libc++abi.dylib                       0x189ab2bd4 operator new(unsigned long) + 32
0   libsystem_malloc.dylib                0x189933a68 _malloc_zone_malloc_instrumented_or_legacy + 148
====
    8 (3.00K) ROOT CYCLE: <std::__shared_ptr_emplace<gtdynamics::Link> 0x13f7040f0> [624]
       CYCLE BACK TO <std::__shared_ptr_emplace<gtdynamics::Link> 0x13f7040f0> [624]
       7 (2.39K) ROOT CYCLE: <malloc in std::shared_ptr<gtsam::ConstVarFactor>* std::vector<std::shared_ptr<gtsam::ConstVarFactor>>::__push_back_slow_path<std::shared_ptr<gtsam::ConstVarFactor> const&>(std::shared_ptr<gtsam::ConstVarFactor> const&) 0x13f704bb0> [48]
          3 (1.17K) ROOT CYCLE: <std::__shared_ptr_emplace<gtdynamics::RevoluteJoint> 0x13f7046b0> [544]
             CYCLE BACK TO <std::__shared_ptr_emplace<gtdynamics::Link> 0x13f7040f0> [624]
             2 (656 bytes) ROOT CYCLE: <std::__shared_ptr_emplace<gtdynamics::Link> 0x142806f80> [624]
                1 (32 bytes) ROOT CYCLE: <malloc in std::shared_ptr<gtsam::ConstVarFactor>* std::vector<std::shared_ptr<gtsam::ConstVarFactor>>::__push_back_slow_path<std::shared_ptr<gtsam::ConstVarFactor> const&>(std::shared_ptr<gtsam::ConstVarFactor> const&) 0x1428074b0> [32]
          3 (1.17K) ROOT CYCLE: <std::__shared_ptr_emplace<gtdynamics::RevoluteJoint> 0x13f704940> [544]
             CYCLE BACK TO <std::__shared_ptr_emplace<gtdynamics::Link> 0x13f7040f0> [624]
             2 (656 bytes) ROOT CYCLE: <std::__shared_ptr_emplace<gtdynamics::Link> 0x13f704360> [624]
                1 (32 bytes) ROOT CYCLE: <malloc in std::shared_ptr<gtsam::ConstVarFactor>* std::vector<std::shared_ptr<gtsam::ConstVarFactor>>::__push_back_slow_path<std::shared_ptr<gtsam::ConstVarFactor> const&>(std::shared_ptr<gtsam::ConstVarFactor> const&) 0x13f704920> [32]

STACK OF 1 INSTANCE OF 'ROOT CYCLE: <malloc in std::shared_ptr<gtsam::ConstVarFactor>* std::vector<std::shared_ptr<gtsam::ConstVarFactor>>::__push_back_slow_path<std::shared_ptr<gtsam::ConstVarFactor> const&>(std::shared_ptr<gtsam::ConstVarFactor> const&)>':
8   dyld                                  0x18976f154 start + 2476
7   testForwardKinematicsFactor           0x102783a34 main + 28
6   testForwardKinematicsFactor           0x102789b48 TestRegistry::run(TestResult&) + 140
5   testForwardKinematicsFactor           0x10278304c ForwardKinematicsFactorArbitraryTimeTest::run(TestResult&) + 156
4   libgtdynamics.dylib                   0x102e36e68 gtdynamics::CreateRobotFromFile(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, bool) + 620
3   libgtdynamics.dylib                   0x102e37648 gtdynamics::ExtractRobotFromSdf(sdf::v12::Model const&) + 940
2   libgtdynamics.dylib                   0x102e385b8 std::__1::shared_ptr<gtsam::ConstVarFactor>* std::__1::vector<std::__1::shared_ptr<gtsam::ConstVarFactor>, std::__1::allocator<std::__1::shared_ptr<gtsam::ConstVarFactor>>>::__push_back_slow_path<std::__1::shared_ptr<gtsam::ConstVarFactor> const&>(std::__1::shared_ptr<gtsam::ConstVarFactor> const&) + 108
1   libc++abi.dylib                       0x189ab2bd4 operator new(unsigned long) + 32
0   libsystem_malloc.dylib                0x189933a68 _malloc_zone_malloc_instrumented_or_legacy + 148
====
    5 (1.81K) ROOT CYCLE: <malloc in std::shared_ptr<gtsam::ConstVarFactor>* std::vector<std::shared_ptr<gtsam::ConstVarFactor>>::__push_back_slow_path<std::shared_ptr<gtsam::ConstVarFactor> const&>(std::shared_ptr<gtsam::ConstVarFactor> const&) 0x13f728cb0> [32]
       4 (1.78K) ROOT CYCLE: <std::__shared_ptr_emplace<gtdynamics::RevoluteJoint> 0x142516a80> [544]
          2 (656 bytes) ROOT CYCLE: <std::__shared_ptr_emplace<gtdynamics::Link> 0x1425164c0> [624]
             1 (32 bytes) ROOT CYCLE: <malloc in std::shared_ptr<gtsam::ConstVarFactor>* std::vector<std::shared_ptr<gtsam::ConstVarFactor>>::__push_back_slow_path<std::shared_ptr<gtsam::ConstVarFactor> const&>(std::shared_ptr<gtsam::ConstVarFactor> const&) 0x13f729df0> [32]
          1 (624 bytes) ROOT CYCLE: <std::__shared_ptr_emplace<gtdynamics::Link> 0x142516730> [624]
             CYCLE BACK TO <malloc in std::shared_ptr<gtsam::ConstVarFactor>* std::vector<std::shared_ptr<gtsam::ConstVarFactor>>::__push_back_slow_path<std::shared_ptr<gtsam::ConstVarFactor> const&>(std::shared_ptr<gtsam::ConstVarFactor> const&) 0x13f728cb0> [32]



Binary Images:
       0x102778000 -        0x10278bfff +testForwardKinematicsFactor (0) <DB6C85A3-E8F1-3F9D-9A00-EDC670F255EA> /Users/*/testForwardKinematicsFactor
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       0x102d74000 -        0x102d77fff +libboost_chrono-mt.dylib (0) <FB5CB409-B0B1-3FD4-8B30-8511FE8E0423> /opt/homebrew/*/libboost_chrono-mt.dylib
       0x102d8c000 -        0x102d93fff +liburdfdom_sensor.3.0.dylib (0) <D3A28050-369D-3E20-83DF-CC266DE30921> /opt/homebrew/*/liburdfdom_sensor.3.0.dylib
       0x102da0000 -        0x102da7ffb +liburdfdom_model_state.3.0.dylib (0) <1BF7D86A-A480-3149-8D1A-5DE167E825D9> /opt/homebrew/*/liburdfdom_model_state.3.0.dylib
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       0x102ddc000 -        0x102de7ff3 +libtinyxml2.9.0.0.dylib (0) <2D7CBB13-5019-36FC-A216-207951A9CE30> /opt/homebrew/*/libtinyxml2.9.0.0.dylib
       0x102dfc000 -        0x102f0fff3 +libgtdynamics.dylib (0) <303300B6-F623-3A49-8A11-7319B2893CE3> /Users/*/libgtdynamics.dylib
       0x102fe0000 -        0x103017ff7 +libboost_regex-mt.dylib (0) <6946F778-9CE6-3319-9BB2-3A4EED8DABEF> /opt/homebrew/*/libboost_regex-mt.dylib
       0x103040000 -        0x10304bfff +libtbbmalloc.2.13.dylib (0) <DB9E4154-080D-3781-8187-C707CF552422> /opt/homebrew/*/libtbbmalloc.2.13.dylib
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       0x103510000 -        0x10381ffff +libgtsam.4.3a0.dylib (0) <DB65AE8C-03D3-340D-8AFB-5B2D5588CF2E> /Users/*/libgtsam.4.3a0.dylib
       0x103a54000 -        0x103c57ffb +libsdformat12.12.7.2.dylib (0) <3150A738-5277-30A1-8945-89E42AF5A2C0> /opt/homebrew/*/libsdformat12.12.7.2.dylib
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       0x189718000 -        0x189768e0b  libobjc.A.dylib (912.7) <5C6386BD-F308-3370-BCE9-63D1A89DAB87> /usr/lib/libobjc.A.dylib
       0x189769000 -        0x1897f2507  dyld (1.0.0 - 1165.3) <F635824E-318B-3F0C-842C-C369737F2B68> /usr/lib/dyld
       0x1897f3000 -        0x1897f7ff8  libsystem_blocks.dylib (90) <6BC23DD4-94AC-3BB0-BC84-93E6D7813ACE> /usr/lib/system/libsystem_blocks.dylib
       0x1897f8000 -        0x189842fff  libxpc.dylib (2748.140.10) <987AF6AA-AB54-39CE-84CF-C6D2D1DC9464> /usr/lib/system/libxpc.dylib
       0x189843000 -        0x18985dfff  libsystem_trace.dylib (1510.140.4) <72852AF1-4BCC-326A-BE13-6C6F22A44E4A> /usr/lib/system/libsystem_trace.dylib
       0x18985e000 -        0x189907fcf  libcorecrypto.dylib (1638.140.6) <717EA919-DB53-3DDA-AFA1-D87BFD649A83> /usr/lib/system/libcorecrypto.dylib
       0x189908000 -        0x189944ff7  libsystem_malloc.dylib (521.120.7) <8A69A1AC-6D54-3B64-9860-CD0DB47473ED> /usr/lib/system/libsystem_malloc.dylib
       0x189945000 -        0x18998cfff  libdispatch.dylib (1477.100.9) <1A1CE00A-89CD-36BA-9678-5038AEDD0D8D> /usr/lib/system/libdispatch.dylib
       0x18998d000 -        0x18998ffff  libsystem_featureflags.dylib (86) <F9E56A3B-6350-3D8B-BEC6-6BC253B19355> /usr/lib/system/libsystem_featureflags.dylib
       0x189990000 -        0x189a0eff7  libsystem_c.dylib (1592.100.35) <D30F1830-93D0-3D0B-8CBA-9544E84BFD5B> /usr/lib/system/libsystem_c.dylib
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       0x189a9c000 -        0x189ab7ffb  libc++abi.dylib (1700.255.5) <68E3EB36-B4BA-30E0-A240-31E942936D06> /usr/lib/libc++abi.dylib
       0x189ab8000 -        0x189af2ffb  libsystem_kernel.dylib (10063.141.2) <71FF45B8-F14E-3666-9E96-6CF58315B91D> /usr/lib/system/libsystem_kernel.dylib
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       0x18f1ea000 -        0x18f204fff  libsystem_networkextension.dylib (1838.140.5.0.1) <9ADD8A04-8F8C-3916-A9ED-20F6947294BD> /usr/lib/system/libsystem_networkextension.dylib
       0x18f27d000 -        0x18f294ff7  libsystem_asl.dylib (398) <138939F9-52A2-35BF-A8E5-4B2154A3F1B0> /usr/lib/system/libsystem_asl.dylib
       0x190c6f000 -        0x190c77ff3  libsystem_symptoms.dylib (1871.140.6) <3E5E0270-E98C-303F-A566-624005886B88> /usr/lib/system/libsystem_symptoms.dylib
       0x193dfd000 -        0x193e27ffb  libsystem_containermanager.dylib (582.140.2) <230DEE13-0738-3710-A305-2D87D2522E52> /usr/lib/system/libsystem_containermanager.dylib
       0x194dc1000 -        0x194dc5fff  libsystem_configuration.dylib (1300.120.2) <4F21FA09-0224-337E-9843-10109C019B1E> /usr/lib/system/libsystem_configuration.dylib
       0x194dc6000 -        0x194dcbfff  libsystem_sandbox.dylib (2190.140.13) <DA843F8C-6155-3B7C-99B0-DEB74CF9F109> /usr/lib/system/libsystem_sandbox.dylib
       0x195be9000 -        0x195bebfff  libquarantine.dylib (172.140.2) <1F514E6F-7D94-356E-A5DC-6E8DCDD40846> /usr/lib/system/libquarantine.dylib
       0x1963a0000 -        0x1963a5fff  libsystem_coreservices.dylib (152.5.3) <CF38F1DD-9C1B-34D8-8C4D-DC5899486CD1> /usr/lib/system/libsystem_coreservices.dylib
       0x1966ce000 -        0x196704ff3  libsystem_m.dylib (3252.100.9) <0BE2E009-9F7F-331D-B4AC-F39136591F6F> /usr/lib/system/libsystem_m.dylib
       0x196709000 -        0x196710ffb  libmacho.dylib (1010.6) <BB441E41-3804-3949-B620-0B29D7975490> /usr/lib/system/libmacho.dylib
       0x196731000 -        0x19673eff7  libcommonCrypto.dylib (600028.100.1) <B0A2DDA7-420D-3DDE-9FE2-3AFDD2188F14> /usr/lib/system/libcommonCrypto.dylib
       0x19673f000 -        0x19674afff  libunwind.dylib (1700.242) <40A5125B-1225-337B-9D1A-968356D29580> /usr/lib/system/libunwind.dylib
       0x19674b000 -        0x196752fff  liboah.dylib (318.9) <749BB71D-B6F2-3C9D-A96D-65D22F7A42B3> /usr/lib/liboah.dylib
       0x196753000 -        0x19675cfff  libcopyfile.dylib (196.120.5) <3F3A181E-C6AB-3F09-BC74-37B8AC2BBE57> /usr/lib/system/libcopyfile.dylib
       0x19675d000 -        0x196760fff  libcompiler_rt.dylib (103.2) <D133BCC9-EFB7-3C69-83D2-A33BB6AFA430> /usr/lib/system/libcompiler_rt.dylib
       0x196761000 -        0x196765ffb  libsystem_collections.dylib (1592.100.35) <E08997D8-CC79-3A51-A3E0-B7706A78CC50> /usr/lib/system/libsystem_collections.dylib
       0x196766000 -        0x196769ffb  libsystem_secinit.dylib (147.140.2) <1F043FF2-1603-32F0-A8FB-DC6CBB118581> /usr/lib/system/libsystem_secinit.dylib
       0x19676a000 -        0x19676cffb  libremovefile.dylib (70.100.4) <01FAC88B-53F2-36C6-91EE-1EC62AC11CC8> /usr/lib/system/libremovefile.dylib
       0x19676d000 -        0x19676dffb  libkeymgr.dylib (31) <59B09DF8-56B7-3FAC-94D3-CC946797E98E> /usr/lib/system/libkeymgr.dylib
       0x19676e000 -        0x196776fff  libsystem_dnssd.dylib (2200.140.11) <4E11F9C6-8BD5-380C-A46F-7AB5DD6E91B6> /usr/lib/system/libsystem_dnssd.dylib
       0x196777000 -        0x19677cfff  libcache.dylib (93) <291EEBA0-190B-30E0-A7FF-1ED0CA3505B4> /usr/lib/system/libcache.dylib
       0x19677d000 -        0x19677efff  libSystem.B.dylib (1345.120.2) <2C0809B3-B3E0-3921-BB57-569E6984EC1A> /usr/lib/libSystem.B.dylib
       0x1af494000 -        0x1af49ffff  com.apple.MallocStackLogging (1.0 - 64565.70.2) <996FAAAE-AA80-3D57-BBE4-727436BAF450> /System/Library/PrivateFrameworks/MallocStackLogging.framework/Versions/A/MallocStackLogging
       0x251671000 -        0x251674fff  libsystem_darwindirectory.dylib (86.0.2) <815D7896-79A3-36C4-8008-DD672DA625C5> /usr/lib/system/libsystem_darwindirectory.dylib
       0x251675000 -        0x251678fff  libsystem_eligibility.dylib (47.140.3) <ADF6A9D2-C5C3-3A9C-9302-4618D9DFAD21> /usr/lib/system/libsystem_eligibility.dylib
       0x251679000 -        0x25167cffb  libsystem_sanitizers.dylib (8) <6BBDFCBC-D608-3318-BC22-2172E5258046> /usr/lib/system/libsystem_sanitizers.dylib

The issue here is that we have a reference cycle of shared pointers, one from Joint to Link and another one from Link to Joint. This can cause orphaned cycles to be leaked.

The fix for this is to use a std::weak_ptr which I have done for the child_link_ and parent_link_ in the Joint class.

After the updates, I get the following memory leak report:

leaks --atExit -- ./testForwardKinematicsFactor
testForwardKinematicsFactor(8235) MallocStackLogging: could not tag MSL-related memory as no_footprint, so those pages will be included in process footprint - (null)
testForwardKinematicsFactor(8235) MallocStackLogging: recording malloc and VM allocation stacks using lite mode
There were no test failures
Process:         testForwardKinematicsFactor [8235]
Path:            /Users/USER/*/testForwardKinematicsFactor
Load Address:    0x100cb4000
Identifier:      testForwardKinematicsFactor
Version:         0
Code Type:       ARM64
Platform:        macOS
Parent Process:  leaks [8234]

Date/Time:       2024-10-22 09:58:38.896 -0400
Launch Time:     2024-10-22 09:58:38.086 -0400
OS Version:      macOS 14.6.1 (23G93)
Report Version:  7
Analysis Tool:   /Applications/Xcode.app/Contents/Developer/usr/bin/leaks
Analysis Tool Version:  Xcode 16.0 (16A242d)

Physical footprint:         10.8M
Physical footprint (peak):  28.4M
Idle exit:                  untracked
----

leaks Report Version: 4.0, multi-line stacks
Process 8235: 250 nodes malloced for 39 KB
Process 8235: 0 leaks for 0 total leaked bytes.

@varunagrawal varunagrawal self-assigned this Oct 22, 2024
dellaert
dellaert approved these changes Oct 22, 2024
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Awesome!

tests/testPoseFactor.cpp Outdated
@@ -49,7 +49,8 @@ TEST(PoseFactor, error) {
Pose3 cMp = Pose3(Rot3(), Point3(-2, 0, 0));
Vector6 screw_axis;
screw_axis << 0, 0, 1, 0, 1, 0;
auto joint = make_joint(cMp, screw_axis);
auto joint_and_links = make_joint(cMp, screw_axis);
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auto [joint, links] = ?

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Thank you. Updated!

@varunagrawal varunagrawal merged commit 5caf4ec into master Oct 22, 2024
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@varunagrawal varunagrawal deleted the fix-memory-leak branch October 22, 2024 19:15
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@dellaert dellaert dellaert approved these changes

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@varunagrawal @dellaert